The two federally designated cancer centers in the Boston area are embarking on an unusual alliance that will combine the research strengths of both organizations to yield new treatments and insights into two highly lethal cancers.

Researchers at the David H. Koch Institute for Integrative Cancer Research at MIT and the Dana-Farber/Harvard Cancer Center have collaborated in the past, but the so-called bridge project being unveiled Tuesday is intended to spark increased cross-Charles teamwork.

An initial $2.6 million round of funding, provided by foundations and philanthropists, will support two years of work by four research teams pursuing new approaches to pancreatic cancer and glioblastoma, an aggressive brain cancer. The project leaders hope to raise $50 million over the next three to five years to support multidiscplinary, multi-institutional research teams studying problems related to those and other cancers.

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Linda Weiss, director of the Office of Cancer Centers at the National Cancer Institute, said that as the guidelines for cancer centers are being revised, more emphasis will be put on such partnerships.

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“We are in fact moving in that direction and will be recognizing those kinds of collaborations much more strongly,’’ Weiss said. “Collaboration, I think, becomes very important, both for bringing in alternative perspectives and alternative expertise, but also for really moving things through the translational pipeline’’ and into the clinic.

The groundwork for the bridge project was laid last year at two standing-room-only meetings held on the home turf of both organizations. Clinicians and scientists from the Dana-Farber/Harvard Cancer Center came to Kendall Square in Cambridge to talk about the challenges and opportunities in pancreatic cancer and glioblastoma. Scientists and engineers from the Koch Institute traveled to the Longwood Medical Area in Boston to present some of the new technologies being developed in their laboratories.

“We needed to educate our scientists and engineers about the clinical barriers and opportunities, and likewise we needed to educate our clinical colleagues about what are the technologies that could be brought to bear,’’ said Tyler Jacks, director of the Koch Institute.

J. Christopher Love, an associate professor in chemical engineering at the Massachusetts Institute of Technology, said that it was after one of those meetings that he began to talk with two Dana-Farber scientists he had never worked with before about the possible cancer applications of a technology that he had used to investigate questions about infectious disease, autoimmunity, and food allergies.

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Love’s “nanowell’’ technology, which he compares to an ice cube tray at the smallest scale, allows researchers to study the function of single cells. Dr. Matthew Meyerson of Dana-Farber Cancer Institute had been working on sequencing genomes of single cells. Dr. Keith Ligon at Dana-Farber specialized in studying the biology of glioblastoma.

The combined forces of the scientists’ knowledge and technology will provide new ways to probe the diversity among individual cells in glioblastoma, which might reveal more about how to more effectively treat the deadly cancer.

“The right collaborations are very catalytic; you develop better technologies than we would as an engineering group alone,’’ Love said.

Other efforts focus on new approaches to pancreatic cancer, including a stent that could release chemotherapy, and an effort to develop ways to get the immune system to fight cancer.

“What makes this exciting is the opportunity to step back and to look at these questions in a different way, with some new insights,’’ said Dr. Jeffrey Clark, an associate professor of medicine at Harvard Medical School and Massachusetts General Hospital who is working on the stent project with a bioengineer and a cardiologist.